private IAtomContainer ParseSmiles(string smiles, bool isRxnPart)
{
try
{
// create the Beam object from the SMILES
Beam.Graph g = Beam.Graph.FromSmiles(smiles);
// convert the Beam object model to the CDK - note exception thrown
// if a kekule structure could not be assigned.
var mol = beamToCDK.ToAtomContainer(Kekulise ? g.Kekule() : g, Kekulise);
if (!isRxnPart)
{
try
{
// CXSMILES layer
ParseMolCXSMILES(g.Title, mol);
}
catch (Exception e)
{
// e.StackTrace
throw new InvalidSmilesException($"Error parsing CXSMILES: {e.Message}");
}
}
return(mol);
}
catch (IOException e)
{
throw new InvalidSmilesException($"could not parse '{smiles}', {e.Message}");
}
catch (Exception)
{
throw new InvalidSmilesException($"could not parse '{smiles}'");
}
}
IAtomContainer Convert(string smi)
{
BeamToCDK g2c = new BeamToCDK(CDK.Builder);
Graph g = Graph.FromSmiles(smi);
return(g2c.ToAtomContainer(g, false));
}
private IAtomContainer ParseSmiles(string smiles, bool isRxnPart)
{
try
{
// create the Beam object from parsing the SMILES
var warnings = new HashSet <string>();
var g = Beam.Graph.Parse(smiles, Strict, warnings);
foreach (var warning in warnings)
{
Trace.TraceWarning(warning);
}
// convert the Beam object model to the CDK - note exception thrown
// if a kekule structure could not be assigned.
var mol = beamToCDK.ToAtomContainer(Kekulise ? g.Kekule() : g, Kekulise);
if (!isRxnPart)
{
try
{
// CXSMILES layer
ParseMolCXSMILES(g.Title, mol);
}
catch (Exception e)
{
// e.StackTrace
throw new InvalidSmilesException($"Error parsing CXSMILES: {e.Message}", e);
}
}
return(mol);
}
catch (IOException e)
{
throw new InvalidSmilesException($"could not parse '{smiles}', {e.Message}", e);
}
catch (Exception e)
{
throw new InvalidSmilesException($"could not parse '{smiles}'", e);
}
}
